ISEC Hidden Markov Model: Morning Tutorial

Welcome to the morning tutorial!

We will begin with a 30-minute introduction that will provide an overview of what are hidden Markov models (HMMs) and then we will complete together the activity found in the Tutorial_files folder. The tutorial has some guided activities.

During most of the tutorial, we will look at a narwhal dataset provided by Dr. Marianne Marcoux. The narwhals have been tagged in Tremblay Sound, Nunavut, Canada. We will look at their movement over a two-week duration.

Photo Credits: Paul Nicklen

Workshop learning objectives

• Understanding the statistical framework for HMMs and their applications to animal movement data
• Being able to fit HMMs to animal movement data to identify behaviours
• Being able to incorporate covariates on state transition probability to identify conditions that promote different behaviours
• Being able to integrate covariates on emission probabilities to model biased random walks

Preparation/instructions

• Download and unzip workshop zip from Github
• Install all the required packages as described in 0_Installing_packages.Rmd
• Make sure all packages are up-to-date as older versions may not work
• Modify the R Markdown file R Markdown file (.Rmd) provided or create a new R or R Markdown file in the ISEC2024_HMM_workshop directory and follow along with the tutorial html file.

Let’s go !